Take the Flour Back and other GM protest groups were thwarted at Rothamsted on 27 May, and the tone of the debate has changed. Photograph: Paul Hackett/Reuters

'No GM spuds," proclaimed a banner wielded by protesters in opposition to a trial of genetically modified crops last weekend. The activists had planned to destroy the trial plots at Rothamsted Research in Hertfordshire but were thwarted by a low turnout and a well-prepared police presence.

But more interesting than their failure to vandalise the plants is the important turning point in the GM debate that this trial has revealed. Media reporting and comment has been mostly neutral and positive about the experiments, or actively hostile to the protesters – a far cry from the days of "Frankenfood" headlines. What has changed?

In the GM debates of the late 90s and early 2000s, the mega-agricultural companies pushing GM seemed to have a tin ear to legitimate concerns about the health effects of their products and the danger they might pose to the environment. It was easy for the activists (the plucky little guys) to play to those fears in opposition to Monsanto et al (the faceless mercenary corporate interests). In the argument over the Rothamsted trial, the playbook has been reversed.

First, instead of hiding, the scientists have been out in the open. By explaining their research to journalists at the Science Media Centre in London in March they could not be accused of keeping the trial secret. When activists announced their plan to destroy the crop, the researchers adopted a new tactic. Rather than condemning the threats and hunkering down, they issued a plaintive YouTube appeal. The video is not PR-slick or well-rehearsed; the researchers come across as genuine in their desire simply to find out the answers. Their message to the activists was to discuss the issues rather than resort to criminal damage.

The scientists have been keen to point out that the risk of pollen from their wheat reaching surrounding crops is vanishingly small because the crop is self-fertilising. So the urgency – claimed by the protesters – to stop a trial that could have profound effects on the environment simply did not exist. Also vital to the researchers' argument is that they are not Monsanto. The research is publicly funded, and the scientists have promised that the results will not be patented. So familiar jibes that the scientists are only in it for the money have missed their mark.

Something else which has changed is that genetic modification is no longer new. GM crops have been grown commercially around the world for more than a decade, and have been eaten by millions. Scary health effects that were always the most potent fears for average consumers (though perhaps also the least credible) have failed to materialise. And while the impact of GM crops has been far from benign in all instances, the logic that every case of manipulating plant genes is bad and dangerous is now demonstrably false.

Despite acres of coverage and glorious sunshine, the protest failed to really take off. There were an estimated 200 people at the event. But their seemingly fanatical opposition to the GM trial set against the reason and openness of the scientists has cast the whole GM debate in a new light.